Then I dont know why it would open a new ticket unless they are not replying to the last email they got from the system, or if they are using an email client that doesn't properly follow the email RFCs and utilize the message-id header.

Not sure it's related, but we had this happen with 1.8 or 1.9. We used GMail web client most of the time and the replies by email would not work. If I used Thunderbird or Outlook clients connected to my GMail account, the replies would work.